Origin IGS: gtgtgtcggtaaggaagcttgccgatagaaccccaccacgccacccggaagagggtggcgggtggtatctctatccttcaaacaaaaaacatgctgacgt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 acgtcagcatgttttttgtttgaaggatagagataccacccgccaccctcttccgggtggcgtggtggggttctatcggcaagcttccttaccgacacac Mask Tandem Repeat Region ================================================ gtgtgtcggtaaggaagcttgccgatagaaccccaccacgccacccggaagagggtggcgggtggtatctctatccttcaaacaaaaaacatgctgacgt Find is-nt database================================================ Query_seq: PG0328:PG0329|PG0328:PG0329:imidazolonepropionase:formiminotransferase-cyclodeaminase-related protein:<-<-:363517..363616 100 gtgtgtcggtaaggaagcttgccgatagaaccccaccacgccacccggaagagggtggcgggtggtatctctatccttcaaacaaaaaacatgctgacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PG0328:PG0329|PG0328:PG0329:imidazolonepropionase:formiminotransferase-cyclodeaminase-related protein:<-<-:363517..363616 100 gtgtgtcggtaaggaagcttgccgatagaaccccaccacgccacccggaagagggtggcgggtggtatctctatccttcaaacaaaaaacatgctgacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PG0328:PG0329|PG0328:PG0329:imidazolonepropionase:formiminotransferase-cyclodeaminase-related protein:<-<-:363517..363616 100 gtgtgtcggtaaggaagcttgccgatagaaccccaccacgccacccggaagagggtggcgggtggtatctctatccttcaaacaaaaaacatgctgacgt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 gtgtgtcggtaaggaagcttgccgatagaaccccaccacgccacccggaagagggtggcgggtggtatctctatccttcaaacaaaaaacatgctgacgt Predict ORF larger than 30AA ================================================ Protein_Len: 32 Strand: + Start: 3 End: 98 .. M S V R K L A D R T P P R H P E E G G G W Y L Y P S N K K H A D .. gtgtgtcggtaaggaagcttgccgatagaaccccaccacgccacccggaagagggtggcgggtggtatctctatccttcaaacaaaaaacatgctgacgt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ gtgtgtcggtaaggaagcttgccgatagaaccccaccacgccacccggaagagggtggcgggtggtatctctatccttcaaacaaaaaacatgctgacgt Predict TransTerm conf > 70================================================ TransTerm Strand: - Conf: 79 HP_score: -12.3 Tail_Score: -3.48395 Start: 31 End: 67 Full_Region: tttgaaggatagaga taccacccgccaccc tcttcc gggtggcgtggtgggg ttctatcggcaagct ..............................taccacccgccaccctcttccgggtggcgtggtgggg................................. TransTerm Strand: + Conf: 87 HP_score: -17.1 Tail_Score: -3.08278 Start: 33 End: 65 Full_Region: CTTGCCGATAGAACC CCACCACGCCACCC GGAAGA GGGTGGCGGGTGG TATCTCTATCCTTCA ................................CCACCACGCCACCCGGAAGAGGGTGGCGGGTGG................................... Find igs database================================================ Query_seq: PG0328:PG0329|PG0328:PG0329:imidazolonepropionase:formiminotransferase-cyclodeaminase-related protein:<-<-:363517..363616 100 gtgtgtcggtaaggaagcttgccgatagaaccccaccacgccacccggaagagggtggcgggtggtatctctatccttcaaacaaaaaacatgctgacgt Intra-Species Hit: Count: 1 Min: 1 Max: 100 Len: 100 Subject: NC_002950_PG0328_PG0329|imidazolonepropionase:formiminotransferase- cyclodeaminase-related protein|NEGATIVE:NEGATIVE|[363517,363616]|100 HSP 1 e-value: 2.0E-50 bit: 198.0 Len: 100 Query Start:1 Query End:100 Subject Strand: POSITIVE Subject Start: 1 Subject End: 100 gtgtgtcggtaaggaagcttgccgatagaaccccaccacgccacccggaagagggtggcgggtggtatctctatccttcaaacaaaaaacatgctgacgt gtgtgtcggtaaggaagcttgccgatagaaccccaccacgccacccggaagagggtggcgggtggtatctctatccttcaaacaaaaaacatgctgacgt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ GUGUGUCGGUAAGGAAGCUUGCCGAUAGAACCCCACCACGCCACCCGGAAGAGGGUGGCGGGUGGUAUCUCUAUCCUUCAAACAAAAAACAUGCUGACGU ((((((.((((((....))))))((((((...(((((.((((((((......)))))))))))))....)))))).............))))))...... (-45.60) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ ACGUCAGCAUGUUUUUUGUUUGAAGGAUAGAGAUACCACCCGCCACCCUCUUCCGGGUGGCGUGGUGGGGUUCUAUCGGCAAGCUUCCUUACCGACACAC ..(((............(((((...(((((((...(((((((((((((......)))))))).)))))..)))))))..))))).........))).... (-42.90) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 1170 70 21 161 112 NC_002950:PG0328|5end_imidazolonepropionase_363426..363656_NEGATIVE 479 75 31 58 15 NC_002950:PG0265|5end_hypothetical_protein_298551..298781_NEGATIVE 433 75 31 58 15 NC_002950:PG0493|5end_hypothetical_protein_534900..535130_NEGATIVE 397 80 32 85 35 NC_002950:PG2037|5end_hypothetical_protein_2137812..2138042_NEGATIVE 394 58 11 204 166 NC_002950:PG0137|5end_aminoacyl-histidine_dipeptidase_159104..159334_POSITIVE 385 66 29 59 24 NC_002950:PG0638|5end_tetraacyldisaccharide_4'-kinase_691183..691413_NEGATIVE 365 79 36 102 38 NC_002950:PG0842|5end_mobilizable_transposon,_hypothetical_protein,_putative_904874..905104_NEGATIVE 362 48 3 224 181 NC_002950:PG1498|5end_hypothetical_protein_1574656..1574886_POSITIVE 361 59 13 58 2 NC_002950:PG0714|5end_copper_homeostasis_protein_CutC_768671..768901_NEGATIVE 358 75 31 58 15 NC_002950:PG1426|5end_hypothetical_protein_1511310..1511540_NEGATIVE 357 59 13 124 69 NC_002950:PG1441|5end_lysozyme-related_protein_1527525..1527755_NEGATIVE 357 65 21 103 59 NC_002950:PG0145|5end_hypothetical_protein_167831..168061_POSITIVE 355 70 25 54 5 NC_002950:PG0949|5end_hypothetical_protein_1008686..1008916_POSITIVE 354 67 27 60 14 NC_002950:PG1621|5end_hypothetical_protein_1701431..1701661_NEGATIVE 351 59 16 164 120 NC_002950:PG1479|5end_conjugative_transposon_protein_TraJ_1555234..1555464_NEGATIVE 350 79 39 59 18 NC_002950:PG1255|5end_recombination_protein_RecR_1332751..1332981_NEGATIVE 349 66 21 78 27 NC_002950:PG2107|5end_thiamine_biosynthesis_protein_ThiH_2216658..2216888_NEGATIVE 349 70 21 191 145 NC_002950:PG2028|5end_ebsC_protein_2126027..2126257_POSITIVE 347 75 36 223 181 NC_002950:PG2223|5end_glycosyl_transferase,_group_2_family_protein_2337713..2337943_POSITIVE 346 77 33 176 131 NC_002950:PG1947|5end_TPR_domain_protein_2032932..2033162_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 515 66 21 142 97 NC_002950:PG1497|3end_DNA-binding_protein,_histone-like_family_1574635..1574785_POSITIVE 413 69 36 132 97 NC_002950:PG0746|3end_sensor_histidine_kinase_792536..792686_NEGATIVE 409 65 21 89 31 NC_002950:PG1359|3end_hypothetical_protein_1437644..1437794_NEGATIVE 397 80 32 88 38 NC_002950:PG2038|3end_N-acetylmuramoyl-L-alanine_amidase,_putative_2137809..2137959_NEGATIVE 385 59 14 83 38 NC_002950:PG1733|3end_hypothetical_protein_1821186..1821336_NEGATIVE 384 66 36 77 33 NC_002950:PG1721|3end_ribonuclease_R_1812472..1812622_POSITIVE 375 79 31 78 15 NC_002950:PG0143|3end_hydrolase,_carbon-nitrogen_family_165747..165897_NEGATIVE 369 69 21 85 20 NC_002950:PG0605|3end_hypothetical_protein_661165..661315_NEGATIVE 365 79 36 105 41 NC_002950:PG0843|3end_hypothetical_protein_904871..905021_NEGATIVE 360 70 21 79 12 NC_002950:PG1020|3end_hypothetical_protein_1083458..1083608_POSITIVE 354 67 27 73 27 NC_002950:PG1622|3end_DNA_topoisomerase_IV_subunit_A_1701418..1701568_NEGATIVE 351 59 16 132 88 NC_002950:PG1480|3end_conjugative_transposon_protein_TraI_1555266..1555416_NEGATIVE 351 64 22 149 102 NC_002950:PG0330|3end_DNA-binding_protein,_histone-like_family_364478..364628_NEGATIVE 350 79 39 62 21 NC_002950:PG1256|3end_ribonuclease,_Rne/Rng_family_1332748..1332898_NEGATIVE 349 66 21 65 14 NC_002950:PG2108|3end_thiazole_synthase_2216671..2216821_NEGATIVE 345 67 23 63 13 NC_002950:PG0715|3end_transporter_768676..768826_NEGATIVE 344 58 13 59 9 NC_002950:PG2127|3end_hypothetical_protein_2233109..2233259_NEGATIVE 342 70 21 90 43 NC_002950:PG1288|3end_GDP-mannose_4,6-dehydratase_1367128..1367278_POSITIVE 340 65 21 150 105 NC_002950:PG0736|3end_ribonuclease_HII_786293..786443_POSITIVE 336 49 1 89 46 NC_002950:PG2050|3end_hypothetical_protein_2149159..2149309_NEGATIVE